Host-like RNA Elements Regulate Virus Translation

Abstract

Viruses are obligate, intracellular parasites that co-opt host cell machineries for propagation. Critical among these machineries are those that translate RNA into protein and their mechanisms of control. Most regulatory mechanisms effectuate their activity by targeting sequence or structural features at the RNA termini, i.e., at the 5' or 3' ends, including the untranslated regions (UTRs). Translation of most eukaryotic mRNAs is initiated by 5' cap-dependent scanning. In contrast, many viruses initiate translation at internal RNA regions at internal ribosome entry sites (IRESs). Eukaryotic mRNAs often contain upstream open reading frames (uORFs) that permit condition-dependent control of downstream major ORFs. To offset genome compression and increase coding capacity, some viruses take advantage of out-of-frame overlapping uORFs (oORFs). Lacking the essential machinery of protein synthesis, for example, ribosomes and other translation factors, all viruses utilize the host apparatus to generate virus protein. In addition, some viruses exhibit RNA elements that bind host regulatory factors that are not essential components of the translation machinery. SARS-CoV-2 is a paradigm example of a virus taking advantage of multiple features of eukaryotic host translation control: the virus mimics the established human GAIT regulatory element and co-opts four host aminoacyl tRNA synthetases to form a stimulatory binding complex. Utilizing discontinuous transcription, the elements are present and identical in all SARS-CoV-2 subgenomic RNAs (and the genomic RNA). Thus, the virus exhibits a post-transcriptional regulon that improves upon analogous eukaryotic regulons, in which a family of functionally related mRNA targets contain elements that are structurally similar but lacking sequence identity. This "thrifty" virus strategy can be exploited against the virus since targeting the element can suppress the expression of all subgenomic RNAs as well as the genomic RNA. Other 3' end viral elements include 3'-cap-independent translation elements (3'-CITEs) and 3'-tRNA-like structures. Elucidation of virus translation control elements, their binding proteins, and their mechanisms can lead to novel therapeutic approaches to reduce virus replication and pathogenicity.

Keywords: RNA element; SARS-CoV-2; internal ribosome entry sites; translation control; untranslated region; upstream open reading frames; virus; virus-host interaction.

Figure 1

Translation in viruses is regulated by themes shared with hosts. Various RNA elements shown here are IRES (Internal Ribosome Entry Site), uORF (upstream Open Reading Frame), oORF (overlapping Open Reading Frame), TURBS (Termination Upstream Ribosome Binding Site), VAIT (Virus Activated Inhibitor of Translation element), 3′-CITE (3′-Cap Independent Translation Enhancer), SPEAR (Sarbecoviral Pan-End Activating RNA element), and 3′TLS (3′ tRNA-Like Structure) that can be charged with amino acid (aa). IRESs and 3′-CITEs are diverse, as discussed in the text. 3′-CITEs and VAIT activate and inhibit virus translation in a 5′-end dependent manner, as shown with dashed lines.

Figure 2

A unique regulon in viruses that employ discontinuous transcription can regulate genomic and sub-genomic RNAs. As an example, a simplified schematic of the SPEAR regulon of SARS-CoV-2 is shown. L: 5′-leader (within solid black arrows) that resides in the 5′UTR, gRNA: genomic RNA, sgRNA: subgenomic RNA. Frameshift element between ORF1a and ORF1b is shown in grey. Green, brown and blue dashed lines represent sgRNA-generating events between identical transcription regulatory sequences contained in 5′-leader and in nucleotides 5′ to ORFs encoded in sgRNA1 (green), sgRNA2 (blue), sgRNA3 (brown) and so on. The genomic terminus, common to gRNA and sgRNAs, reportedly pairs with the 5′-leader (darker gray dashed line). 5′-3′ communication through the SPEAR element is yet unknown (lighter gray dashed line).